Starting phenix.real_space_refine on Wed Sep 17 03:20:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bh0_44528/09_2025/9bh0_44528.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bh0_44528/09_2025/9bh0_44528.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bh0_44528/09_2025/9bh0_44528.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bh0_44528/09_2025/9bh0_44528.map" model { file = "/net/cci-nas-00/data/ceres_data/9bh0_44528/09_2025/9bh0_44528.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bh0_44528/09_2025/9bh0_44528.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 20 5.16 5 C 1940 2.51 5 N 458 2.21 5 O 516 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2934 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 2925 Classifications: {'peptide': 390} Link IDs: {'PTRANS': 16, 'TRANS': 373} Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 1.07, per 1000 atoms: 0.36 Number of scatterers: 2934 At special positions: 0 Unit cell: (69.139, 60.809, 79.968, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 20 16.00 O 516 8.00 N 458 7.00 C 1940 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.34 Conformation dependent library (CDL) restraints added in 154.3 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 712 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 0 sheets defined 88.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'A' and resid 2 through 22 Processing helix chain 'A' and resid 23 through 27 Processing helix chain 'A' and resid 28 through 59 removed outlier: 4.030A pdb=" N GLY A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE A 42 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL A 43 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N VAL A 44 " --> pdb=" O LYS A 40 " (cutoff:3.500A) Proline residue: A 45 - end of helix Processing helix chain 'A' and resid 60 through 94 removed outlier: 3.609A pdb=" N ARG A 66 " --> pdb=" O LYS A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 121 Processing helix chain 'A' and resid 126 through 134 Processing helix chain 'A' and resid 135 through 154 removed outlier: 3.782A pdb=" N GLY A 154 " --> pdb=" O LEU A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 180 removed outlier: 3.720A pdb=" N LYS A 180 " --> pdb=" O ASP A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 197 Processing helix chain 'A' and resid 198 through 203 removed outlier: 3.502A pdb=" N LEU A 202 " --> pdb=" O GLY A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 223 Processing helix chain 'A' and resid 223 through 230 Processing helix chain 'A' and resid 235 through 254 removed outlier: 5.328A pdb=" N GLU A 245 " --> pdb=" O LYS A 241 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N ALA A 246 " --> pdb=" O LYS A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 271 Proline residue: A 261 - end of helix removed outlier: 3.502A pdb=" N GLU A 268 " --> pdb=" O MET A 264 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLU A 269 " --> pdb=" O ARG A 265 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLY A 271 " --> pdb=" O ALA A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 288 removed outlier: 3.604A pdb=" N PHE A 279 " --> pdb=" O SER A 275 " (cutoff:3.500A) Proline residue: A 282 - end of helix removed outlier: 3.867A pdb=" N THR A 286 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 307 removed outlier: 3.504A pdb=" N TYR A 307 " --> pdb=" O VAL A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 330 Processing helix chain 'A' and resid 335 through 349 removed outlier: 4.163A pdb=" N THR A 342 " --> pdb=" O LEU A 338 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N MET A 343 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL A 344 " --> pdb=" O MET A 340 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER A 347 " --> pdb=" O MET A 343 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL A 348 " --> pdb=" O VAL A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 360 removed outlier: 4.236A pdb=" N ALA A 356 " --> pdb=" O LEU A 352 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU A 357 " --> pdb=" O GLU A 353 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLY A 360 " --> pdb=" O ALA A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 388 removed outlier: 3.758A pdb=" N LEU A 365 " --> pdb=" O ILE A 361 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA A 368 " --> pdb=" O ILE A 364 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU A 378 " --> pdb=" O VAL A 374 " (cutoff:3.500A) 232 hydrogen bonds defined for protein. 690 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.47 Time building geometry restraints manager: 0.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 897 1.34 - 1.46: 633 1.46 - 1.58: 1418 1.58 - 1.70: 0 1.70 - 1.81: 37 Bond restraints: 2985 Sorted by residual: bond pdb=" N ASP A1000 " pdb=" CA ASP A1000 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.64e+00 bond pdb=" CB GLU A 26 " pdb=" CG GLU A 26 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.21e+00 bond pdb=" N ILE A 104 " pdb=" CA ILE A 104 " ideal model delta sigma weight residual 1.474 1.458 0.017 1.57e-02 4.06e+03 1.15e+00 bond pdb=" N VAL A 272 " pdb=" CA VAL A 272 " ideal model delta sigma weight residual 1.468 1.461 0.008 1.05e-02 9.07e+03 5.45e-01 bond pdb=" CA GLU A 26 " pdb=" CB GLU A 26 " ideal model delta sigma weight residual 1.529 1.542 -0.013 1.78e-02 3.16e+03 5.03e-01 ... (remaining 2980 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.11: 3863 1.11 - 2.23: 149 2.23 - 3.34: 25 3.34 - 4.46: 15 4.46 - 5.57: 3 Bond angle restraints: 4055 Sorted by residual: angle pdb=" CA GLU A 26 " pdb=" CB GLU A 26 " pdb=" CG GLU A 26 " ideal model delta sigma weight residual 114.10 119.67 -5.57 2.00e+00 2.50e-01 7.75e+00 angle pdb=" N GLY A 154 " pdb=" CA GLY A 154 " pdb=" C GLY A 154 " ideal model delta sigma weight residual 111.24 115.23 -3.99 1.49e+00 4.50e-01 7.18e+00 angle pdb=" N THR A 286 " pdb=" CA THR A 286 " pdb=" C THR A 286 " ideal model delta sigma weight residual 114.56 111.16 3.40 1.27e+00 6.20e-01 7.16e+00 angle pdb=" C LEU A 221 " pdb=" N ILE A 222 " pdb=" CA ILE A 222 " ideal model delta sigma weight residual 122.66 120.46 2.20 9.70e-01 1.06e+00 5.15e+00 angle pdb=" CB GLU A 26 " pdb=" CG GLU A 26 " pdb=" CD GLU A 26 " ideal model delta sigma weight residual 112.60 116.32 -3.72 1.70e+00 3.46e-01 4.78e+00 ... (remaining 4050 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.93: 1570 15.93 - 31.86: 155 31.86 - 47.80: 36 47.80 - 63.73: 16 63.73 - 79.66: 1 Dihedral angle restraints: 1778 sinusoidal: 668 harmonic: 1110 Sorted by residual: dihedral pdb=" CA ILE A 42 " pdb=" C ILE A 42 " pdb=" N VAL A 43 " pdb=" CA VAL A 43 " ideal model delta harmonic sigma weight residual -180.00 -159.75 -20.25 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA ILE A 104 " pdb=" C ILE A 104 " pdb=" N HIS A 105 " pdb=" CA HIS A 105 " ideal model delta harmonic sigma weight residual -180.00 -162.56 -17.44 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CB MET A 247 " pdb=" CG MET A 247 " pdb=" SD MET A 247 " pdb=" CE MET A 247 " ideal model delta sinusoidal sigma weight residual -60.00 -3.47 -56.53 3 1.50e+01 4.44e-03 9.40e+00 ... (remaining 1775 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 316 0.028 - 0.055: 121 0.055 - 0.083: 61 0.083 - 0.110: 13 0.110 - 0.138: 5 Chirality restraints: 516 Sorted by residual: chirality pdb=" CA ILE A 104 " pdb=" N ILE A 104 " pdb=" C ILE A 104 " pdb=" CB ILE A 104 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.75e-01 chirality pdb=" CA ILE A 234 " pdb=" N ILE A 234 " pdb=" C ILE A 234 " pdb=" CB ILE A 234 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.82e-01 chirality pdb=" CA VAL A 333 " pdb=" N VAL A 333 " pdb=" C VAL A 333 " pdb=" CB VAL A 333 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.68e-01 ... (remaining 513 not shown) Planarity restraints: 492 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 109 " -0.023 5.00e-02 4.00e+02 3.44e-02 1.89e+00 pdb=" N PRO A 110 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 110 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 110 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 265 " -0.110 9.50e-02 1.11e+02 4.94e-02 1.71e+00 pdb=" NE ARG A 265 " 0.009 2.00e-02 2.50e+03 pdb=" CZ ARG A 265 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 265 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 265 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 110 " 0.004 2.00e-02 2.50e+03 8.59e-03 7.38e-01 pdb=" C PRO A 110 " -0.015 2.00e-02 2.50e+03 pdb=" O PRO A 110 " 0.006 2.00e-02 2.50e+03 pdb=" N ASN A 111 " 0.005 2.00e-02 2.50e+03 ... (remaining 489 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 25 2.64 - 3.20: 3007 3.20 - 3.77: 4576 3.77 - 4.33: 6085 4.33 - 4.90: 10223 Nonbonded interactions: 23916 Sorted by model distance: nonbonded pdb=" N GLU A 269 " pdb=" OE1 GLU A 269 " model vdw 2.071 3.120 nonbonded pdb=" OG SER A 114 " pdb=" OE1 GLU A 117 " model vdw 2.296 3.040 nonbonded pdb=" O ALA A 326 " pdb=" OG1 THR A 330 " model vdw 2.300 3.040 nonbonded pdb=" O ASN A 111 " pdb=" OD1 ASN A 111 " model vdw 2.430 3.040 nonbonded pdb=" O ARG A 265 " pdb=" OE1 GLU A 269 " model vdw 2.480 3.040 ... (remaining 23911 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.130 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2985 Z= 0.142 Angle : 0.573 5.569 4055 Z= 0.324 Chirality : 0.037 0.138 516 Planarity : 0.004 0.049 492 Dihedral : 14.286 79.660 1066 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.32 % Allowed : 16.46 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.89 (0.44), residues: 388 helix: 2.38 (0.29), residues: 309 sheet: None (None), residues: 0 loop : 0.07 (0.79), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 265 TYR 0.013 0.001 TYR A 4 PHE 0.009 0.001 PHE A 239 TRP 0.004 0.001 TRP A 192 HIS 0.001 0.001 HIS A 109 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 2985) covalent geometry : angle 0.57252 ( 4055) hydrogen bonds : bond 0.14759 ( 232) hydrogen bonds : angle 5.63422 ( 690) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 91 time to evaluate : 0.110 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.6364 (OUTLIER) cc_final: 0.6155 (mmt) REVERT: A 6 LYS cc_start: 0.8609 (mtmt) cc_final: 0.8387 (mtmt) REVERT: A 40 LYS cc_start: 0.8401 (mttt) cc_final: 0.7524 (pttt) REVERT: A 62 LYS cc_start: 0.9072 (mmtt) cc_final: 0.8684 (tptm) REVERT: A 94 LYS cc_start: 0.8579 (mttm) cc_final: 0.8245 (mtmt) REVERT: A 169 GLU cc_start: 0.8216 (mm-30) cc_final: 0.8002 (mt-10) REVERT: A 171 MET cc_start: 0.8126 (mmm) cc_final: 0.7905 (mmt) REVERT: A 223 VAL cc_start: 0.8469 (t) cc_final: 0.8124 (m) REVERT: A 254 CYS cc_start: 0.9097 (m) cc_final: 0.8539 (m) REVERT: A 286 THR cc_start: 0.8798 (p) cc_final: 0.8566 (t) REVERT: A 340 MET cc_start: 0.8702 (mmp) cc_final: 0.8290 (tpp) REVERT: A 362 ASP cc_start: 0.8244 (t70) cc_final: 0.7867 (t0) REVERT: A 387 THR cc_start: 0.8529 (m) cc_final: 0.8234 (p) outliers start: 1 outliers final: 0 residues processed: 91 average time/residue: 0.0735 time to fit residues: 7.8378 Evaluate side-chains 85 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 84 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 24 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 37 optimal weight: 0.3980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.089317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.079791 restraints weight = 5537.435| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 1.86 r_work: 0.2950 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 2985 Z= 0.209 Angle : 0.611 5.428 4055 Z= 0.318 Chirality : 0.043 0.131 516 Planarity : 0.004 0.031 492 Dihedral : 4.657 40.892 410 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 4.11 % Allowed : 15.82 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.33 (0.42), residues: 388 helix: 2.03 (0.28), residues: 320 sheet: None (None), residues: 0 loop : -0.76 (0.77), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 37 TYR 0.014 0.002 TYR A 197 PHE 0.019 0.002 PHE A 27 TRP 0.005 0.002 TRP A 192 HIS 0.004 0.002 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00495 ( 2985) covalent geometry : angle 0.61142 ( 4055) hydrogen bonds : bond 0.05461 ( 232) hydrogen bonds : angle 4.48013 ( 690) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.070 Fit side-chains revert: symmetry clash REVERT: A 40 LYS cc_start: 0.8618 (mttt) cc_final: 0.7935 (pttt) REVERT: A 62 LYS cc_start: 0.8788 (mmtt) cc_final: 0.8529 (mmmt) REVERT: A 126 ASN cc_start: 0.8442 (t0) cc_final: 0.8162 (t0) REVERT: A 129 GLU cc_start: 0.8268 (tt0) cc_final: 0.8017 (tt0) REVERT: A 169 GLU cc_start: 0.8622 (mm-30) cc_final: 0.8399 (mt-10) REVERT: A 171 MET cc_start: 0.8450 (mmm) cc_final: 0.8164 (mmt) REVERT: A 221 LEU cc_start: 0.7889 (OUTLIER) cc_final: 0.7621 (mm) REVERT: A 223 VAL cc_start: 0.8836 (t) cc_final: 0.8541 (m) REVERT: A 254 CYS cc_start: 0.9080 (m) cc_final: 0.8823 (m) REVERT: A 286 THR cc_start: 0.9139 (p) cc_final: 0.8901 (t) REVERT: A 340 MET cc_start: 0.9007 (mmp) cc_final: 0.8747 (tpp) outliers start: 13 outliers final: 7 residues processed: 91 average time/residue: 0.0673 time to fit residues: 7.2056 Evaluate side-chains 85 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 333 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 16 optimal weight: 0.3980 chunk 29 optimal weight: 0.6980 chunk 4 optimal weight: 0.0060 chunk 1 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 0 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 11 optimal weight: 0.0570 chunk 23 optimal weight: 0.9990 overall best weight: 0.3314 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.090920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.081108 restraints weight = 5417.732| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 1.87 r_work: 0.2976 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2985 Z= 0.150 Angle : 0.557 5.315 4055 Z= 0.289 Chirality : 0.041 0.142 516 Planarity : 0.004 0.031 492 Dihedral : 4.133 22.464 407 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 4.11 % Allowed : 18.99 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.35 (0.42), residues: 388 helix: 2.04 (0.28), residues: 321 sheet: None (None), residues: 0 loop : -0.83 (0.80), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 386 TYR 0.014 0.002 TYR A 75 PHE 0.023 0.002 PHE A 27 TRP 0.005 0.001 TRP A 192 HIS 0.003 0.001 HIS A 5 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 2985) covalent geometry : angle 0.55697 ( 4055) hydrogen bonds : bond 0.04637 ( 232) hydrogen bonds : angle 4.25559 ( 690) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.134 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 LYS cc_start: 0.8727 (mmtt) cc_final: 0.8407 (mmmm) REVERT: A 104 ILE cc_start: 0.7803 (mt) cc_final: 0.7320 (tt) REVERT: A 126 ASN cc_start: 0.8445 (t0) cc_final: 0.8224 (t0) REVERT: A 133 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7825 (mm-30) REVERT: A 169 GLU cc_start: 0.8612 (mm-30) cc_final: 0.8387 (mt-10) REVERT: A 171 MET cc_start: 0.8376 (mmm) cc_final: 0.8151 (mmt) REVERT: A 221 LEU cc_start: 0.7859 (OUTLIER) cc_final: 0.7635 (mt) REVERT: A 223 VAL cc_start: 0.8812 (t) cc_final: 0.8526 (m) REVERT: A 254 CYS cc_start: 0.9007 (m) cc_final: 0.8747 (m) REVERT: A 286 THR cc_start: 0.9100 (p) cc_final: 0.8871 (t) REVERT: A 340 MET cc_start: 0.8987 (mmp) cc_final: 0.8753 (tpp) outliers start: 13 outliers final: 8 residues processed: 85 average time/residue: 0.0673 time to fit residues: 6.9387 Evaluate side-chains 82 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 317 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 10 optimal weight: 3.9990 chunk 22 optimal weight: 0.3980 chunk 16 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 11 optimal weight: 0.1980 chunk 25 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 6 optimal weight: 0.4980 chunk 20 optimal weight: 0.3980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.090644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.080777 restraints weight = 5403.188| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 1.85 r_work: 0.2972 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 2985 Z= 0.166 Angle : 0.546 5.298 4055 Z= 0.284 Chirality : 0.041 0.131 516 Planarity : 0.004 0.033 492 Dihedral : 4.113 23.499 407 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 4.43 % Allowed : 19.62 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.40 (0.43), residues: 388 helix: 2.01 (0.28), residues: 324 sheet: None (None), residues: 0 loop : -0.53 (0.87), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 37 TYR 0.011 0.002 TYR A 197 PHE 0.024 0.002 PHE A 279 TRP 0.005 0.001 TRP A 192 HIS 0.003 0.001 HIS A 5 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 2985) covalent geometry : angle 0.54648 ( 4055) hydrogen bonds : bond 0.04564 ( 232) hydrogen bonds : angle 4.19675 ( 690) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.124 Fit side-chains revert: symmetry clash REVERT: A 104 ILE cc_start: 0.7758 (mt) cc_final: 0.7313 (tt) REVERT: A 133 GLU cc_start: 0.8071 (mm-30) cc_final: 0.7828 (mm-30) REVERT: A 223 VAL cc_start: 0.8826 (t) cc_final: 0.8550 (m) REVERT: A 340 MET cc_start: 0.9021 (mmp) cc_final: 0.8780 (tpp) outliers start: 14 outliers final: 7 residues processed: 81 average time/residue: 0.0649 time to fit residues: 6.3737 Evaluate side-chains 76 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 317 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 31 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 chunk 38 optimal weight: 0.3980 chunk 32 optimal weight: 0.4980 chunk 19 optimal weight: 0.9990 chunk 6 optimal weight: 0.4980 chunk 26 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.090341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.080378 restraints weight = 5180.549| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 1.83 r_work: 0.2965 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 2985 Z= 0.195 Angle : 0.574 5.443 4055 Z= 0.301 Chirality : 0.042 0.129 516 Planarity : 0.005 0.037 492 Dihedral : 4.143 24.096 407 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 4.43 % Allowed : 21.20 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.34 (0.43), residues: 388 helix: 2.02 (0.28), residues: 322 sheet: None (None), residues: 0 loop : -0.79 (0.85), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 37 TYR 0.013 0.002 TYR A 4 PHE 0.024 0.002 PHE A 279 TRP 0.003 0.001 TRP A 192 HIS 0.003 0.001 HIS A 5 Details of bonding type rmsd covalent geometry : bond 0.00473 ( 2985) covalent geometry : angle 0.57353 ( 4055) hydrogen bonds : bond 0.04706 ( 232) hydrogen bonds : angle 4.24649 ( 690) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.108 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 ILE cc_start: 0.7817 (mt) cc_final: 0.7377 (tt) REVERT: A 133 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7902 (mm-30) REVERT: A 169 GLU cc_start: 0.8621 (mm-30) cc_final: 0.8298 (tt0) REVERT: A 223 VAL cc_start: 0.8865 (t) cc_final: 0.8601 (m) REVERT: A 340 MET cc_start: 0.9059 (mmp) cc_final: 0.8806 (tpp) REVERT: A 383 ILE cc_start: 0.8862 (OUTLIER) cc_final: 0.8609 (mp) outliers start: 14 outliers final: 8 residues processed: 80 average time/residue: 0.0641 time to fit residues: 6.2139 Evaluate side-chains 78 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 383 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 26 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 4 optimal weight: 0.2980 chunk 23 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.089873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.079928 restraints weight = 5308.929| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 1.84 r_work: 0.2948 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 2985 Z= 0.213 Angle : 0.582 5.497 4055 Z= 0.305 Chirality : 0.042 0.126 516 Planarity : 0.005 0.041 492 Dihedral : 4.178 23.586 407 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 4.11 % Allowed : 22.47 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.23 (0.43), residues: 388 helix: 1.94 (0.28), residues: 323 sheet: None (None), residues: 0 loop : -0.82 (0.87), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 369 TYR 0.013 0.002 TYR A 4 PHE 0.025 0.002 PHE A 27 TRP 0.002 0.001 TRP A 192 HIS 0.003 0.001 HIS A 5 Details of bonding type rmsd covalent geometry : bond 0.00516 ( 2985) covalent geometry : angle 0.58225 ( 4055) hydrogen bonds : bond 0.04845 ( 232) hydrogen bonds : angle 4.28075 ( 690) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.112 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 ILE cc_start: 0.7794 (mt) cc_final: 0.7361 (tt) REVERT: A 126 ASN cc_start: 0.8414 (t0) cc_final: 0.8184 (t0) REVERT: A 133 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7921 (mm-30) REVERT: A 223 VAL cc_start: 0.8840 (t) cc_final: 0.8587 (m) REVERT: A 367 MET cc_start: 0.8274 (mtt) cc_final: 0.8031 (mtm) REVERT: A 383 ILE cc_start: 0.8855 (OUTLIER) cc_final: 0.8601 (mp) outliers start: 13 outliers final: 10 residues processed: 85 average time/residue: 0.0670 time to fit residues: 6.8020 Evaluate side-chains 82 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 383 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 35 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 14 optimal weight: 0.2980 chunk 20 optimal weight: 0.7980 chunk 38 optimal weight: 0.1980 chunk 23 optimal weight: 0.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.090581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.080648 restraints weight = 5304.761| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 1.82 r_work: 0.2966 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 2985 Z= 0.186 Angle : 0.582 5.569 4055 Z= 0.304 Chirality : 0.041 0.128 516 Planarity : 0.005 0.043 492 Dihedral : 4.109 23.204 407 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 4.43 % Allowed : 22.15 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.30 (0.43), residues: 388 helix: 2.00 (0.28), residues: 323 sheet: None (None), residues: 0 loop : -0.88 (0.88), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 238 TYR 0.012 0.001 TYR A 4 PHE 0.026 0.002 PHE A 27 TRP 0.003 0.001 TRP A 192 HIS 0.003 0.001 HIS A 5 Details of bonding type rmsd covalent geometry : bond 0.00449 ( 2985) covalent geometry : angle 0.58239 ( 4055) hydrogen bonds : bond 0.04637 ( 232) hydrogen bonds : angle 4.23068 ( 690) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.104 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 ILE cc_start: 0.7805 (mt) cc_final: 0.7364 (tt) REVERT: A 126 ASN cc_start: 0.8446 (t0) cc_final: 0.8214 (t0) REVERT: A 133 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7926 (mm-30) REVERT: A 169 GLU cc_start: 0.8621 (mm-30) cc_final: 0.8298 (tt0) REVERT: A 223 VAL cc_start: 0.8842 (t) cc_final: 0.8573 (m) REVERT: A 383 ILE cc_start: 0.8826 (OUTLIER) cc_final: 0.8581 (mp) outliers start: 14 outliers final: 12 residues processed: 84 average time/residue: 0.0587 time to fit residues: 6.0317 Evaluate side-chains 84 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 383 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 25 optimal weight: 0.1980 chunk 12 optimal weight: 0.0010 chunk 5 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 22 optimal weight: 0.0010 chunk 10 optimal weight: 0.0030 chunk 35 optimal weight: 0.0870 chunk 38 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 4 optimal weight: 0.4980 overall best weight: 0.0580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.094394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.084244 restraints weight = 5342.523| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 1.90 r_work: 0.3030 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2985 Z= 0.127 Angle : 0.569 7.131 4055 Z= 0.294 Chirality : 0.039 0.132 516 Planarity : 0.004 0.045 492 Dihedral : 3.899 23.584 407 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Rotamer: Outliers : 3.48 % Allowed : 23.42 % Favored : 73.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.79 (0.44), residues: 388 helix: 2.32 (0.28), residues: 322 sheet: None (None), residues: 0 loop : -0.55 (0.90), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 265 TYR 0.016 0.001 TYR A 4 PHE 0.028 0.002 PHE A 27 TRP 0.007 0.002 TRP A 192 HIS 0.001 0.000 HIS A 5 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 2985) covalent geometry : angle 0.56930 ( 4055) hydrogen bonds : bond 0.03740 ( 232) hydrogen bonds : angle 4.01753 ( 690) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.113 Fit side-chains revert: symmetry clash REVERT: A 104 ILE cc_start: 0.7815 (mt) cc_final: 0.7360 (tt) REVERT: A 126 ASN cc_start: 0.8395 (t0) cc_final: 0.8177 (t0) REVERT: A 129 GLU cc_start: 0.8311 (tt0) cc_final: 0.8063 (tt0) REVERT: A 133 GLU cc_start: 0.8132 (mm-30) cc_final: 0.7891 (mm-30) REVERT: A 223 VAL cc_start: 0.8800 (t) cc_final: 0.8512 (m) REVERT: A 383 ILE cc_start: 0.8863 (OUTLIER) cc_final: 0.8593 (mp) outliers start: 11 outliers final: 5 residues processed: 78 average time/residue: 0.0675 time to fit residues: 6.2980 Evaluate side-chains 79 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 383 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 2 optimal weight: 0.4980 chunk 8 optimal weight: 0.1980 chunk 23 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 12 optimal weight: 0.0770 chunk 32 optimal weight: 0.0980 chunk 19 optimal weight: 0.8980 chunk 11 optimal weight: 0.0980 chunk 6 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 overall best weight: 0.1938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.094111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.083888 restraints weight = 5304.782| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 1.85 r_work: 0.3024 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 2985 Z= 0.134 Angle : 0.597 6.992 4055 Z= 0.309 Chirality : 0.040 0.127 516 Planarity : 0.004 0.036 492 Dihedral : 3.782 22.694 407 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 2.85 % Allowed : 25.32 % Favored : 71.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.80 (0.44), residues: 388 helix: 2.30 (0.28), residues: 322 sheet: None (None), residues: 0 loop : -0.44 (0.91), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 238 TYR 0.022 0.001 TYR A 4 PHE 0.031 0.002 PHE A 27 TRP 0.004 0.001 TRP A 192 HIS 0.003 0.001 HIS A 5 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 2985) covalent geometry : angle 0.59729 ( 4055) hydrogen bonds : bond 0.03844 ( 232) hydrogen bonds : angle 4.01491 ( 690) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.067 Fit side-chains revert: symmetry clash REVERT: A 104 ILE cc_start: 0.7806 (mt) cc_final: 0.7348 (tt) REVERT: A 126 ASN cc_start: 0.8428 (t0) cc_final: 0.8223 (t0) REVERT: A 133 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7910 (mm-30) REVERT: A 153 MET cc_start: 0.5379 (mtt) cc_final: 0.5087 (mtt) REVERT: A 223 VAL cc_start: 0.8806 (t) cc_final: 0.8515 (m) REVERT: A 383 ILE cc_start: 0.8811 (OUTLIER) cc_final: 0.8557 (mp) outliers start: 9 outliers final: 6 residues processed: 74 average time/residue: 0.0592 time to fit residues: 5.3262 Evaluate side-chains 73 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 383 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 7 optimal weight: 0.2980 chunk 11 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 22 optimal weight: 0.0370 chunk 4 optimal weight: 0.2980 chunk 28 optimal weight: 0.7980 chunk 0 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 36 optimal weight: 0.2980 overall best weight: 0.3058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.092945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.082761 restraints weight = 5219.324| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 1.85 r_work: 0.3010 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2985 Z= 0.146 Angle : 0.594 6.027 4055 Z= 0.307 Chirality : 0.040 0.125 516 Planarity : 0.004 0.034 492 Dihedral : 3.787 22.647 407 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 3.48 % Allowed : 25.00 % Favored : 71.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.75 (0.44), residues: 388 helix: 2.30 (0.28), residues: 323 sheet: None (None), residues: 0 loop : -0.69 (0.89), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 238 TYR 0.018 0.001 TYR A 4 PHE 0.032 0.002 PHE A 27 TRP 0.005 0.001 TRP A 192 HIS 0.002 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 2985) covalent geometry : angle 0.59392 ( 4055) hydrogen bonds : bond 0.04017 ( 232) hydrogen bonds : angle 4.03930 ( 690) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.074 Fit side-chains revert: symmetry clash REVERT: A 104 ILE cc_start: 0.7781 (mt) cc_final: 0.7312 (tt) REVERT: A 126 ASN cc_start: 0.8436 (t0) cc_final: 0.8227 (t0) REVERT: A 133 GLU cc_start: 0.8131 (mm-30) cc_final: 0.7920 (mm-30) REVERT: A 153 MET cc_start: 0.5484 (mtt) cc_final: 0.5201 (mtt) REVERT: A 179 MET cc_start: 0.8687 (mmp) cc_final: 0.8418 (mmp) REVERT: A 223 VAL cc_start: 0.8817 (t) cc_final: 0.8535 (m) REVERT: A 383 ILE cc_start: 0.8805 (OUTLIER) cc_final: 0.8572 (mp) outliers start: 11 outliers final: 9 residues processed: 79 average time/residue: 0.0584 time to fit residues: 5.6529 Evaluate side-chains 81 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 383 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 31 optimal weight: 0.0970 chunk 11 optimal weight: 0.7980 chunk 14 optimal weight: 0.0980 chunk 0 optimal weight: 0.9990 chunk 17 optimal weight: 0.3980 chunk 33 optimal weight: 0.6980 chunk 8 optimal weight: 0.0970 chunk 15 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 34 optimal weight: 0.2980 overall best weight: 0.1976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.094057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.083758 restraints weight = 5224.832| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 1.89 r_work: 0.3021 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 2985 Z= 0.131 Angle : 0.588 7.266 4055 Z= 0.302 Chirality : 0.040 0.127 516 Planarity : 0.004 0.034 492 Dihedral : 3.761 22.359 407 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Rotamer: Outliers : 3.16 % Allowed : 25.32 % Favored : 71.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.77 (0.43), residues: 388 helix: 2.31 (0.28), residues: 323 sheet: None (None), residues: 0 loop : -0.67 (0.88), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 238 TYR 0.018 0.001 TYR A 4 PHE 0.032 0.002 PHE A 27 TRP 0.005 0.001 TRP A 192 HIS 0.001 0.001 HIS A 5 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 2985) covalent geometry : angle 0.58761 ( 4055) hydrogen bonds : bond 0.03784 ( 232) hydrogen bonds : angle 3.97955 ( 690) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 948.75 seconds wall clock time: 16 minutes 55.87 seconds (1015.87 seconds total)